Time-dependent hydrogen ionisation in the solar chromosphere. I: Methods and first results

An approximate method for solving the rate equations for the hydrogen populations was extended and implemented in the three-dimensional radiation (magneto-)hydrodynamics code CO5BOLD. The method is based on a model atom with six energy levels and fixed radiative rates. It has been tested extensively in one-dimensional simulations. The extended method has been used to create a three-dimensional model that extends from the upper convection zone to the chromosphere. The ionisation degree of hydrogen in our time-dependent simulation is comparable to the corresponding equilibrium value up to 500 km above optical depth unity. Above this height, the non-equilibrium ionisation degree is fairly constant over time and space, and tends to be at a value set by hot propagating shock waves. The hydrogen level populations and electron density are much more constant than the corresponding values for statistical equilibrium, too. In contrast, the equilibrium ionisation degree varies by more than 20 orders of magnitude between hot, shocked regions and cool, non-shocked regions. The simulation shows for the first time in 3D that the chromospheric hydrogen ionisation degree and electron density cannot be calculated in equilibrium. Our simulation can provide realistic values of those quantities for detailed radiative transfer computations.Comment: 8 pages, 7 figure

Is the Sun Lighter than the Earth? Isotopic CO in the Photosphere, Viewed through the Lens of 3D Spectrum Synthesis

We consider the formation of solar infrared (2-6 micron) rovibrational bands of carbon monoxide (CO) in CO5BOLD 3D convection models, with the aim to refine abundances of the heavy isotopes of carbon (13C) and oxygen (18O,17O), to compare with direct capture measurements of solar wind light ions by the Genesis Discovery Mission. We find that previous, mainly 1D, analyses were systematically biased toward lower isotopic ratios (e.g., R23= 12C/13C), suggesting an isotopically "heavy" Sun contrary to accepted fractionation processes thought to have operated in the primitive solar nebula. The new 3D ratios for 13C and 18O are: R23= 91.4 +/- 1.3 (Rsun= 89.2); and R68= 511 +/- 10 (Rsun= 499), where the uncertainties are 1 sigma and "optimistic." We also obtained R67= 2738 +/- 118 (Rsun= 2632), but we caution that the observed 12C17O features are extremely weak. The new solar ratios for the oxygen isotopes fall between the terrestrial values and those reported by Genesis (R68= 530, R6= 2798), although including both within 2 sigma error flags, and go in the direction favoring recent theories for the oxygen isotope composition of Ca-Al inclusions (CAI) in primitive meteorites. While not a major focus of this work, we derive an oxygen abundance of 603 +/- 9 ppm (relative to hydrogen; 8.78 on the logarithmic H= 12 scale). That the Sun likely is lighter than the Earth, isotopically speaking, removes the necessity to invoke exotic fractionation processes during the early construction of the inner solar system

Inter-network regions of the Sun at millimetre wavelengths

The continuum intensity at wavelengths around 1 mm provides an excellent way to probe the solar chromosphere. Future high-resolution millimetre arrays, such as the Atacama Large Millimeter Array (ALMA), will thus produce valuable input for the ongoing controversy on the thermal structure and the dynamics of this layer. Synthetic brightness temperature maps are calculated on basis of three-dimensional radiation (magneto-)hydrodynamic (MHD) simulations. While the millimetre continuum at 0.3mm originates mainly from the upper photosphere, the longer wavelengths considered here map the low and middle chromosphere. The effective formation height increases generally with wavelength and also from disk-centre towards the solar limb. The average intensity contribution functions are usually rather broad and in some cases they are even double-peaked as there are contributions from hot shock waves and cool post-shock regions in the model chromosphere. Taking into account the deviations from ionisation equilibrium for hydrogen gives a less strong variation of the electron density and with it of the optical depth. The result is a narrower formation height range. The average brightness temperature increases with wavelength and towards the limb. The relative contrast depends on wavelength in the same way as the average intensity but decreases towards the limb. The dependence of the brightness temperature distribution on wavelength and disk-position can be explained with the differences in formation height and the variation of temperature fluctuations with height in the model atmospheres.Comment: 15 pages, 10 figures, accepted for publication in A&A (15.05.07

Can we trust elemental abundances derived in late-type giants with the classical 1D stellar atmosphere models?

We compare the abundances of various chemical species as derived with 3D hydrodynamical and classical 1D stellar atmosphere codes in a late-type giant characterized by T_eff=3640K, log g = 1.0, [M/H] = 0.0. For this particular set of atmospheric parameters the 3D-1D abundance differences are generally small for neutral atoms and molecules but they may reach up to 0.3-0.4 dex in case of ions. The 3D-1D differences generally become increasingly more negative at higher excitation potentials and are typically largest in the optical wavelength range. Their sign can be both positive and negative, and depends on the excitation potential and wavelength of a given spectral line. While our results obtained with this particular late-type giant model suggest that 1D stellar atmosphere models may be safe to use with neutral atoms and molecules, care should be taken if they are exploited with ions.Comment: Poster presented at the IAU Symposium 265 "Chemical Abundances in the Universe: Connecting First Stars to Planets", Rio de Janeiro, 10-14 August 2009; 2 pages, 1 figur

High-order aberration compensation with Multi-frame Blind Deconvolution and Phase Diversity image restoration techniques

Context. For accurately measuring intensities and determining magnetic field strengths of small-scale solar (magnetic) structure, knowledge of and compensation for the point spread function is crucial. For images recorded with the Swedish 1-meter Solar Telescope, restoration with Multi-Frame Blind Deconvolution and Joint Phase Diverse Speckle methods lead to remarkable improvements in image quality but granulation contrasts that are too low, indicating additional stray light. Aims. We propose a method to compensate for stray light from high-order atmospheric aberrations not included in MFBD and JPDS processing. Methods. To compensate for uncorrected aberrations, a reformulation of the image restoration process is proposed that allows the average effect of hundreds of high-order modes to be compensated for by relying on Kolmogorov statistics for these modes. The applicability of the method requires simultaneous measurements of Fried's parameter r0. The method is tested with simulations as well as real data and extended to include compensation for conventional stray light. Results. We find that only part of the reduction of granulation contrast in SST images is due to uncompensated high-order aberrations. The remainder is still unaccounted for and attributed to stray light from the atmosphere, the telescope with its re-imaging system and to various high-altitude seeing effects. Conclusions. We conclude that statistical compensation of high-order modes is a viable method to reduce the loss of contrast occurring when a limited number of aberrations is explicitly compensated for with MFBD and JPDS processing. We show that good such compensation is possible with only 10 recorded frames. The main limitation of the method is that already MFBD and JPDS processing introduces high-order compensation that, if not taken into account, can lead to over-compensation.Comment: in press in Astronomy & Astrophysic

Microsecond Unfolding Kinetics of Sheep Prion Protein Reveals an Intermediate that Correlates with Susceptibility to Classical Scrapie

AbstractThe microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94–233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfolding kinetics of ovPrP provides evidence for an intermediate species. However, in contrast to previous results for human PrP, there is no evidence for an intermediate under refolding conditions. Global analysis of the kinetic data, based on a sequential three-state mechanism, quantitatively accounts for all folding and unfolding data as a function of denaturant concentration. The simulations predict that an intermediate accumulates under both folding and unfolding conditions, but is observable only in unfolding experiments because the intermediate is optically indistinguishable from the native state. The relative population of intermediates in two ovPrP variants, both transiently and under destabilizing equilibrium conditions, correlates with their propensities for classical scrapie. The variant susceptible to classical scrapie has a larger population of the intermediate state than the resistant variant. Thus, the susceptible variant should be favored to undergo the PrPC to PrPSc conversion and oligomerization